Mercurial > repos > azuzolo > qiime1_3_0
comparison qiime/collate_alpha.xml @ 0:003162f90751 draft
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| author | azuzolo |
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| date | Wed, 06 Jun 2012 16:40:30 -0400 |
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| -1:000000000000 | 0:003162f90751 |
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| 1 <tool id="collate_alpha" name="collate_alpha" version="1.2.0"> | |
| 2 <description>Collate alpha diversity results</description> | |
| 3 <requirements> | |
| 4 <requirement type="binary">collate_alpha.py</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="python"> | |
| 7 qiime_wrapper.py | |
| 8 --galaxy_outputdir=$output1.extra_files_path | |
| 9 --galaxy_new_files_path='$__new_file_path__' | |
| 10 --galaxy_logfile=$output1 | |
| 11 --galaxy_new_datasets='^\S+\.txt$:txt' | |
| 12 --galaxy_datasetid=$output1.id | |
| 13 collate_alpha.py | |
| 14 --input_path=$input_path.extra_files_path | |
| 15 --output_path='$__new_file_path__' | |
| 16 </command> | |
| 17 <inputs> | |
| 18 <param name="input_path" type="data" format="txt" label="input_path" | |
| 19 help="Input is alpha diversity log file [REQUIRED]"/> | |
| 20 <!--<param name="example_path" type="text" label="example_path" | |
| 21 help="example alpha_diversity analysis file, containing all samples and all metrics to be included in the collated result[Default: chosen automatically (see usage string)]"/>--> | |
| 22 </inputs> | |
| 23 <outputs> | |
| 24 <data format="txt" name="output1" label="${tool.name} on ${on_string}"/> | |
| 25 </outputs> | |
| 26 <tests> | |
| 27 </tests> | |
| 28 <help>This tool concatenates all the files generated by alpha_diversity in order to generate rarefaction curves. The input is therefore the log file generated by alpha_diversity, and the output is a log file listing all the output files, as well as the files themselves. Galaxy must be manually refreshed after running this tool to view all output files. | |
| 29 | |
| 30 For more information, see collate_alpha_ in the Qiime documentation. | |
| 31 | |
| 32 Updated and validated 01/16/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA | |
| 33 | |
| 34 Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN | |
| 35 | |
| 36 .. _collate_alpha: http://qiime.org/scripts/collate_alpha.html</help> | |
| 37 </tool> | |
| 38 |